celltrackR (version 1.2.1)

subtracksByTime: Extract Subtracks Starting at a Specific Time

Description

Obtain all subtracks of i steps (i+1 positions) starting at a given timepoint t.

Usage

subtracksByTime(X, t, i = 1, epsilon = 1e-04, tlo = t, thi = t)

Value

A tracks object is returned which contains all the subtracks of any track in the input tracks object that consist of exactly `i` segments and start at the given timepoint t, OR a tracks object with all the timepoints of any track in the input tracks object that are between tlo and thi.

Arguments

X

Tracks object to obtain subtracks from.

t

Timepoint at which the subtracks should start. This value is ignored if tlo and thi are specified, see below.

i

Subtrack length (in number of steps). Set this to NULL to obtain subtracks of varying length but within a specified interval [tlo, thi] (see below).

epsilon

Small error allowed when comparing timepoints because of numerical inaccuracies, see details. Timepoints in tracks are returned if they are within [tlo-epsilon, thi+epsilon].

tlo, thi

Interval specifying the timepoints to be returned. By default, these are not used and tracks starting at timepoint t with exactly i steps are returned; see details.

Details

If i is specified, the given t is retrieved for all tracks in X that contain that timepoint, and any subtracks starting from that time that have exactly i steps are returned. For numerical reasons, timepoints in the data are allowed to deviate a small amount epsilon from t (because otherwise, equal timepoints can seem unequal because of very small deviations).

If i is set to NULL, subtracks are returned with all timepoints lying in the interval [ tlo - epsilon, thi + epsilon ]. These subtracks do NOT have to be of equal length.

See Also

subtracks to extract all subtracks of a given length, prefixes to extract all subtracks of a given length starting from the first coordinate in each track, selectSteps to extract single steps starting at a fixed timepoint from a subset of trackids, and timePoints to return all timepoints occurring in the dataset.

Examples

## Get all the single steps (i=1) starting at the third timepoint in the T cell tracks.
subT <- subtracksByTime( TCells, timePoints(TCells)[3], 1 )

## These all have the same number of steps:
sapply( subT, nrow )

## Or set i to NULL and return all subtracks within the five first timepoints:
subT2 <- subtracksByTime( TCells, NULL, i = NULL,
  tlo = timePoints( TCells )[1], thi = timePoints( TCells )[5] )

## These are not all the same length:
sapply( subT2, nrow )